Miocene carbonates of the Eratosthenes Seamount, located offshore from Cyprus in the Eastern Mediterranean (ODP Leg 160, Site 966), have been re-analysed. The use of SEDEX sequential extraction to evaluate the nutrient concentrations and of CT-Scan for the identification of large benthic foraminifera has resulted in a more detailed palaeoenvironmental reconstruction and an improved stratigraphic framework. Three intervals are recognised in the succession and are attributed to the lower, middle and upper Miocene, respectively. The lower Miocene interval is dominated by large benthic foraminifera and echinoids. This association colonized the top of the seamount following its uplift from deep-water to the photic zone. The middle Miocene interval is characterised by rhodoliths and corals at its base and near the top, whereas seagrass/seaweed assemblages (with epiphytic foraminifera and hooked coralline-algal crusts) dominate its central part. The upper Miocene is represented by coral reef facies near its base and lagoonal facies toward its top. The succession was deposited in an oligotrophic environment and exhibits a general shallowing-upward trend that was mainly controlled by tectonic activity related to the northward subduction of the African plate. The succession of the Eratosthenes Seamount is characterised by a diverse large benthic foraminifera assemblage in its lower part and by corals in its uppermost part, whereas corallines characterise the central interval. This trend is common in Miocene Mediterranean carbonates and its occurrence on an isolated seamount confirms its connection with the general evolution of the basin. The decline of miogypsinids and lepidocyclinids after the early Miocene is notable because the Eratosthenes Seamount was geographically close to the Indo-Pacific Ocean where both groups also thrived during the middle Miocene. This decline was probably caused by the early Miocene closure of the deep-water connection between the Indo-Pacific and the Mediterranean.